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Hou X, Ga L, Zhang X, Ai J. Advances in the application of logic gates in nanozymes. Anal Bioanal Chem 2024:10.1007/s00216-024-05240-w. [PMID: 38488951 DOI: 10.1007/s00216-024-05240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
Nanozymes are a class of nanomaterials with biocatalytic function and enzyme-like activity, whose advantages include high stability, low cost, and mass production. They can catalyze the substrates of natural enzymes based on specific nanostructures and serve as substitutes for natural enzymes. Their applied research involves a wide range of fields such as biomedicine, environmental governance, agriculture, and food. Molecular logic gates are a new cross-disciplinary discipline, which can simulate the function of silicon circuits on a molecular scale, perform single or multiple input logic operations, and generate logic outputs. A molecular logic gate is a binary operation that converts an input signal into an output signal according to the rules of Boolean logic, generating two signals, a high level, and a low level. The high and low levels represent the "true" and "false" values of the logic gates, and their outputs correspond to "l" and "0" of the molecular logic gates, respectively. The combination of nanozymes and logic gates is a novel and attractive research direction, and the cross-application of the two brings new opportunities and ideas for various fields, such as the construction of efficient biocomputers, intelligent drug delivery systems, and the precise diagnosis of diseases. This review describes the application of logic gates based on nanozymes, which is expected to provide a certain theoretical foundation for researchers' subsequent studies.
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Affiliation(s)
- Xiangru Hou
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China
| | - Lu Ga
- College of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot, 010110, China
| | - Xin Zhang
- College of Chemical Engineering, Inner Mongolia University of Technology, 49 Aimin Road, Hohhot, 010051, China.
| | - Jun Ai
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China.
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Zamoskovtseva AA, Golyshev VM, Kizilova VA, Shevelev GY, Pyshnyi DV, Lomzov AA. Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Adv 2022; 12:6416-6431. [PMID: 35424594 PMCID: PMC8981972 DOI: 10.1039/d2ra00155a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging.
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Affiliation(s)
- Anastasia A. Zamoskovtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, 141701, Russia
| | - Victor M. Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Valeria A. Kizilova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Georgiy Yu. Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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Huang Y, Zhao S, Zhang W, Duan Q, Yan Q, Fu H, Zhong L, Yi G. Multifunctional electrochemical biosensor with "tetrahedral tripods" assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA. RSC Adv 2021; 11:20046-20056. [PMID: 35479883 PMCID: PMC9033681 DOI: 10.1039/d1ra02424h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/23/2021] [Indexed: 01/12/2023] Open
Abstract
Nucleic acids are genetic materials in the human body that play important roles in storing, copying, and transmitting genetic information. Abnormal nucleic acid sequences, base mutations, and genetic changes often lead to cancer and other diseases. Meanwhile, methylated DNA is one of the main epigenetic modifications, which is considered to be an excellent biomarker in the early detection, prognosis, and treatment of cancers. Therefore, a multifunctional electrochemical biosensor was constructed with sturdy tetrahedral tripods, which assisted multiple tandem hairpins through base complementary pairing and effective ultra-sensitive detection of targets (DNA, microRNA, and methylated DNA). In the experiments, experimental conditions were optimized, and different DNA concentrations in serum were detected to verify the sensitivity of the biosensor and the feasibility of this protocol. In addition, microRNA and DNA methylation were detected through different designs of tetrahedral tripods (TTs) that capture probes to prove the superiority of this scheme. A sturdy pyramid structure of TTs extremely enhanced the capture efficiency of targets. The targets triggered the one-step isothermal multi-tandem amplification reaction by incubating multiple hairpin assemblies. To our knowledge, a combination of two parts, which greatly reduced background interference and decreased non-specific substance interference, has appeared for the first time in this paper. Moreover, the load area of electrochemical substances was significantly increased than that in previous studies. This greatly increased the detection range and detection limit of targets. The electrochemical signal responses were generated in freely diffusing hexaammineruthenium(iii) chloride (RuHex). RuHex could adhere to the DNA phosphate backbone by a powerful electrostatic attraction, causing increased current responses. Schematic illustration of the fabricated electrochemical biosensor. TTs assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA.![]()
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Affiliation(s)
- Yuqi Huang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing 400016 PR China
| | - Shuhui Zhao
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing 400016 PR China
| | - Wenxiu Zhang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing 400016 PR China
| | - Qiuyue Duan
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing 400016 PR China
| | - Qi Yan
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing 400016 PR China
| | - Hu Fu
- Clinical Laboratory of Chengdu First People's Hospital Chengdu 610000 PR China
| | - Liang Zhong
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing 400016 PR China
| | - Gang Yi
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University Chongqing 400016 PR China
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Erdem A, Eksin E. Electrochemical Detection of Solution Phase Hybridization Related to Single Nucleotide Mutation by Carbon Nanofibers Enriched Electrodes. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E3377. [PMID: 31623126 PMCID: PMC6829215 DOI: 10.3390/ma12203377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/06/2019] [Accepted: 10/11/2019] [Indexed: 12/16/2022]
Abstract
In the present study, a sensitive and selective impedimetric detection of solution-phase nucleic acid hybridization related to Factor V Leiden (FV Leiden) mutation was performed by carbon nanofibers (CNF) modified screen printed electrodes (SPE). The microscopic and electrochemical characterization of CNF-SPEs was explored in comparison to the unmodified electrodes. Since the FV Leiden mutation is a widespread inherited risk factor predisposing to venous thromboembolism, this study herein aimed to perform the impedimetric detection of FV Leiden mutation by a zip nucleic acid (ZNA) probe-based assay in combination with CNF-SPEs. The selectivity of the assay was then examined against the mutation-free DNA sequences as well as the synthetic PCR samples.
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Affiliation(s)
- Arzum Erdem
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey.
- Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey.
| | - Ece Eksin
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey.
- Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey.
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Yang X, Liu Q, Wen D, Gao M, Zhang D, Jin Q, Kong J, Zhang J. Ultrasensitive fluorescence detection of sequence-specific DNA via labeling hairpin DNA probes for fluorescein o-acrylate polymers. Anal Chim Acta 2019; 1088:144-149. [PMID: 31623710 DOI: 10.1016/j.aca.2019.08.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/12/2019] [Accepted: 08/25/2019] [Indexed: 10/26/2022]
Abstract
Sensitive detection of DNA is conducive to enhance the accuracy of diseases diagnosis and risk prediction. In this work, we report the use of activators generated by electron transfer for atom transfer radical polymerization (AGET ATRP) as a novel on-chip amplification strategy for the fluorescence detection of DNA. More specifically, the target DNA was captured by the on-chip immobilized hairpin DNA probes. Upon hybridization, exposed 3'-N3 of the hairpin was used to attach AGET ATRP initiators onto the silicon surface by click chemistry. Then, numerous fluorescent labeling linked to the end of the probes via the formation of long chain polymers of fluorescein o-acrylate, which in turn amplified the fluorescence signal for DNA detection. Under optimal conditions, it showed a good linear range from 100 fM to 1 μM in DNA detection, with the limit of detection as low as 4.3 fM. Moreover, this strategy showed good detection performance in complex real serum samples, the fluorescence intensity of 0.1 nM tDNA in 1% fetal bovine serum samples was 97.6% of that in Tris-EDTA buffer. Based on its high sensitivity, reduced cost and simplicity, the proposed signal amplification strategy displays translational potential in clinical application.
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Affiliation(s)
- Xinxiu Yang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Qianrui Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, PR China
| | - Dongxiao Wen
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450008, PR China
| | - Meng Gao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Dongjian Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Qiaomei Jin
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, PR China.
| | - Jian Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China; Laboratories of Translational Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, Jiangsu Province, PR China.
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Erdem A, Eksin E. Magnetic beads assay based on Zip nucleic acid for electrochemical detection of Factor V Leiden mutation. Int J Biol Macromol 2018; 125:839-846. [PMID: 30552928 DOI: 10.1016/j.ijbiomac.2018.12.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 01/11/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among people. Development of reliable methods for the detection of SNP is crucial in aspects of molecular diagnosis and personalized medicine. In our study, a genomagnetic assay in combination with zip nucleic acid (ZNA) for electrochemical detection of SNP related to Factor V Leiden mutation. For the first time in the literature, a new generation nucleic acid; ZNA was applied herein for electrochemical monitoring of nucleic acid hybridization. Streptavidin coated magnetic beads (MBs) were used for preparation of samples containing ZNA-DNA hybrid and accordingly, the guanine signal was measured as a response of hybridization related to Factor V Leiden mutation by carbon nanofibers (CNF) modified screen printed electrodes (SPE) and multi-channel screen printed array of electrodes (CNF-MULTI SPEx8). The detection limit (DL) was found to be 3.79 μg/mL (376 nM) and, 11.63 μg/mL (1.624 μM), respectively by CNF-SPE and CNF-MULTI SPEx8. The selectivity of ZNA probe to mutation-free DNA sequences was also investigated in contrast to DNA probe. The applicability of ZNA based magnetic beads assay to sequence selective hybridization related to Factor V Leiden was also tested in synthetic PCR samples.
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Affiliation(s)
- Arzum Erdem
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey.
| | - Ece Eksin
- Faculty of Pharmacy, Analytical Chemistry Department, Ege University, Bornova, Izmir 35100, Turkey; Biotechnology Department, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir 35100, Turkey
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Augspurger EE, Rana M, Yigit MV. Chemical and Biological Sensing Using Hybridization Chain Reaction. ACS Sens 2018; 3:878-902. [PMID: 29733201 DOI: 10.1021/acssensors.8b00208] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.
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